Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate Ac3H11_1227 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1227 Length = 334 Score = 305 bits (782), Expect = 8e-88 Identities = 161/336 (47%), Positives = 227/336 (67%), Gaps = 5/336 (1%) Query: 1 MKLLRSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRS 60 MKLL++ LLAT L AA L P AA AQ+ R I+F + + Q + + F + +A ++ Sbjct: 1 MKLLKT-LLATALVAASLLP-AAHAQE---RTIKFAFQNQKDHPQAQGAQKFADLVAAKT 55 Query: 61 GGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQE 120 GG++ VK F +LG D+Q +AL GG EM V + L K+F ++D PFLF QE Sbjct: 56 GGRIAVKLFPGGTLGGDLQTVSALQGGTVEMTVLNAGILAAQSKEFGIYDFPFLFATPQE 115 Query: 121 ADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPV 180 ADAV DGPFG+KL KL K LVGL YWE GFRNLTNSK+P+ K ED+ G+K+RV+Q+P+ Sbjct: 116 ADAVTDGPFGKKLLDKLQAKNLVGLGYWELGFRNLTNSKKPITKAEDIAGLKIRVIQSPI 175 Query: 181 YIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSP 240 YID+FN GANAVP+ F EL+TAME VDGQENP +TI SSKF EVQKYLT+++H+Y+P Sbjct: 176 YIDLFNALGANAVPMPFPELYTAMEQKAVDGQENPFSTILSSKFAEVQKYLTVTRHMYNP 235 Query: 241 WIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDA 300 V+ SK+++D L+ ++K + +A + F+R SR + ++ LK GMQ++E S A Sbjct: 236 QAVIVSKKFWDSLNPADQKALTDAMAEATTFQRGVSRVQANVALEDLKKAGMQVSEFSPA 295 Query: 301 ELGRMREMVKPAMDKFAADGGADLLNELQGEISKVR 336 EL ++R VKP ++K + GA+ + E+ ++K+R Sbjct: 296 ELDKLRAKVKPVVEKHSEKVGAETVQEVYSTLAKLR 331 Lambda K H 0.317 0.134 0.372 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 307 Number of extensions: 13 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 337 Length of database: 334 Length adjustment: 28 Effective length of query: 309 Effective length of database: 306 Effective search space: 94554 Effective search space used: 94554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory